niwrap-afni 0.6.2__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_afni/afni/v_3d_tcorr1_d.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_TCORR1_D_METADATA = Metadata(
-    id="a49b25e122306e3daa45adb2052372c71e881198.boutiques",
+    id="190174caa84432811da6208110559966e00d4828.boutiques",
     name="3dTcorr1D",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ V_3D_TCORR1_D_METADATA = Metadata(
 
 
 V3dTcorr1DParameters = typing.TypedDict('V3dTcorr1DParameters', {
-    "__STYXTYPE__": typing.Literal["3dTcorr1D"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dTcorr1D"]],
+    "ktaub": bool,
+    "num_threads": typing.NotRequired[int | None],
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "pearson": bool,
+    "quadrant": bool,
+    "spearman": bool,
+    "xset": InputPathType,
+    "y_1d": InputPathType,
+})
+V3dTcorr1DParametersTagged = typing.TypedDict('V3dTcorr1DParametersTagged', {
+    "@type": typing.Literal["afni/3dTcorr1D"],
     "ktaub": bool,
     "num_threads": typing.NotRequired[int | None],
     "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
@@ -24,43 +35,11 @@ V3dTcorr1DParameters = typing.TypedDict('V3dTcorr1DParameters', {
     "xset": InputPathType,
     "y_1d": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dTcorr1D": v_3d_tcorr1_d_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "3dTcorr1D": v_3d_tcorr1_d_outputs,
-    }.get(t)
 
 
 class V3dTcorr1DOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_tcorr1_d(...)`.
+    Output object returned when calling `V3dTcorr1DParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +58,7 @@ def v_3d_tcorr1_d_params(
     pearson: bool = False,
     quadrant: bool = False,
     spearman: bool = False,
-) -> V3dTcorr1DParameters:
+) -> V3dTcorr1DParametersTagged:
     """
     Build parameters.
     
@@ -96,7 +75,7 @@ def v_3d_tcorr1_d_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dTcorr1D",
+        "@type": "afni/3dTcorr1D",
         "ktaub": ktaub,
         "pearson": pearson,
         "quadrant": quadrant,
@@ -126,18 +105,18 @@ def v_3d_tcorr1_d_cargs(
     """
     cargs = []
     cargs.append("3dTcorr1D")
-    if params.get("ktaub"):
+    if params.get("ktaub", False):
         cargs.append("-ktaub")
-    if params.get("num_threads") is not None:
-        cargs.append(str(params.get("num_threads")))
-    if params.get("outputtype") is not None:
-        cargs.append(params.get("outputtype"))
-    if params.get("pearson"):
+    if params.get("num_threads", None) is not None:
+        cargs.append(str(params.get("num_threads", None)))
+    if params.get("outputtype", None) is not None:
+        cargs.append(params.get("outputtype", None))
+    if params.get("pearson", False):
         cargs.append("-pearson")
-    if params.get("quadrant"):
+    if params.get("quadrant", False):
         cargs.append("-quadrant")
-    if params.get("spearman"):
-        cargs.append("-spearman" + execution.input_file(params.get("xset")) + execution.input_file(params.get("y_1d")))
+    if params.get("spearman", False):
+        cargs.append("-spearman" + execution.input_file(params.get("xset", None)) + execution.input_file(params.get("y_1d", None)))
     return cargs
 
 
@@ -156,7 +135,7 @@ def v_3d_tcorr1_d_outputs(
     """
     ret = V3dTcorr1DOutputs(
         root=execution.output_file("."),
-        out_file=execution.output_file(pathlib.Path(params.get("xset")).name + "_correlation.nii.gz"),
+        out_file=execution.output_file(pathlib.Path(params.get("xset", None)).name + "_correlation.nii.gz"),
         out_file_=execution.output_file("out_file"),
     )
     return ret
@@ -164,11 +143,13 @@ def v_3d_tcorr1_d_outputs(
 
 def v_3d_tcorr1_d_execute(
     params: V3dTcorr1DParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dTcorr1DOutputs:
     """
-    Computes the correlation coefficient between each voxel time series in the input
-    3D+time dataset.
+    3dTcorr1D
+    
+    Computes the correlation coefficient between each voxel time series in the
+    input 3D+time dataset.
     
     Author: AFNI Developers
     
@@ -176,10 +157,12 @@ def v_3d_tcorr1_d_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dTcorr1DOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TCORR1_D_METADATA)
     params = execution.params(params)
     cargs = v_3d_tcorr1_d_cargs(params, execution)
     ret = v_3d_tcorr1_d_outputs(params, execution)
@@ -199,8 +182,10 @@ def v_3d_tcorr1_d(
     runner: Runner | None = None,
 ) -> V3dTcorr1DOutputs:
     """
-    Computes the correlation coefficient between each voxel time series in the input
-    3D+time dataset.
+    3dTcorr1D
+    
+    Computes the correlation coefficient between each voxel time series in the
+    input 3D+time dataset.
     
     Author: AFNI Developers
     
@@ -219,8 +204,6 @@ def v_3d_tcorr1_d(
     Returns:
         NamedTuple of outputs (described in `V3dTcorr1DOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_TCORR1_D_METADATA)
     params = v_3d_tcorr1_d_params(
         ktaub=ktaub,
         num_threads=num_threads,
@@ -231,13 +214,13 @@ def v_3d_tcorr1_d(
         xset=xset,
         y_1d=y_1d,
     )
-    return v_3d_tcorr1_d_execute(params, execution)
+    return v_3d_tcorr1_d_execute(params, runner)
 
 
 __all__ = [
     "V3dTcorr1DOutputs",
-    "V3dTcorr1DParameters",
     "V_3D_TCORR1_D_METADATA",
     "v_3d_tcorr1_d",
+    "v_3d_tcorr1_d_execute",
     "v_3d_tcorr1_d_params",
 ]

niwrap_afni/afni/v_3d_tcorr_map.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_TCORR_MAP_METADATA = Metadata(
-    id="79957a8f35e2ff51be99a6621ee7fe05bd18188e.boutiques",
+    id="d5e700a27f2c4c830e5e4a0a98879c4211461ba8.boutiques",
     name="3dTcorrMap",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,27 @@ V_3D_TCORR_MAP_METADATA = Metadata(
 
 
 V3dTcorrMapParameters = typing.TypedDict('V3dTcorrMapParameters', {
-    "__STYXTYPE__": typing.Literal["3dTcorrMap"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dTcorrMap"]],
+    "input": InputPathType,
+    "seed": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "automask": bool,
+    "mean": typing.NotRequired[str | None],
+    "zmean": typing.NotRequired[str | None],
+    "qmean": typing.NotRequired[str | None],
+    "pmean": typing.NotRequired[str | None],
+    "thresh": typing.NotRequired[str | None],
+    "varthresh": typing.NotRequired[str | None],
+    "norm_varthresh": typing.NotRequired[str | None],
+    "corrmap": typing.NotRequired[str | None],
+    "corrmask": bool,
+    "aexpr": typing.NotRequired[str | None],
+    "cexpr": typing.NotRequired[str | None],
+    "sexpr": typing.NotRequired[str | None],
+    "hist": typing.NotRequired[str | None],
+})
+V3dTcorrMapParametersTagged = typing.TypedDict('V3dTcorrMapParametersTagged', {
+    "@type": typing.Literal["afni/3dTcorrMap"],
     "input": InputPathType,
     "seed": typing.NotRequired[InputPathType | None],
     "mask": typing.NotRequired[InputPathType | None],
@@ -33,42 +53,11 @@ V3dTcorrMapParameters = typing.TypedDict('V3dTcorrMapParameters', {
     "sexpr": typing.NotRequired[str | None],
     "hist": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dTcorrMap": v_3d_tcorr_map_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-    }.get(t)
 
 
 class V3dTcorrMapOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_tcorr_map(...)`.
+    Output object returned when calling `V3dTcorrMapParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -92,7 +81,7 @@ def v_3d_tcorr_map_params(
     cexpr: str | None = None,
     sexpr: str | None = None,
     hist: str | None = None,
-) -> V3dTcorrMapParameters:
+) -> V3dTcorrMapParametersTagged:
     """
     Build parameters.
     
@@ -130,7 +119,7 @@ def v_3d_tcorr_map_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dTcorrMap",
+        "@type": "afni/3dTcorrMap",
         "input": input_,
         "automask": automask,
         "corrmask": corrmask,
@@ -181,80 +170,80 @@ def v_3d_tcorr_map_cargs(
     """
     cargs = []
     cargs.append("3dTcorrMap")
-    cargs.append(execution.input_file(params.get("input")))
-    if params.get("seed") is not None:
+    cargs.append(execution.input_file(params.get("input", None)))
+    if params.get("seed", None) is not None:
         cargs.extend([
             "-seed",
-            execution.input_file(params.get("seed"))
+            execution.input_file(params.get("seed", None))
         ])
-    if params.get("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask"))
+            execution.input_file(params.get("mask", None))
         ])
-    if params.get("automask"):
+    if params.get("automask", False):
         cargs.append("-automask")
-    if params.get("mean") is not None:
+    if params.get("mean", None) is not None:
         cargs.extend([
             "-Mean",
-            params.get("mean")
+            params.get("mean", None)
         ])
-    if params.get("zmean") is not None:
+    if params.get("zmean", None) is not None:
         cargs.extend([
             "-Zmean",
-            params.get("zmean")
+            params.get("zmean", None)
         ])
-    if params.get("qmean") is not None:
+    if params.get("qmean", None) is not None:
         cargs.extend([
             "-Qmean",
-            params.get("qmean")
+            params.get("qmean", None)
         ])
-    if params.get("pmean") is not None:
+    if params.get("pmean", None) is not None:
         cargs.extend([
             "-Pmean",
-            params.get("pmean")
+            params.get("pmean", None)
         ])
-    if params.get("thresh") is not None:
+    if params.get("thresh", None) is not None:
         cargs.extend([
             "-Thresh",
-            params.get("thresh")
+            params.get("thresh", None)
         ])
-    if params.get("varthresh") is not None:
+    if params.get("varthresh", None) is not None:
         cargs.extend([
             "-VarThresh",
-            params.get("varthresh")
+            params.get("varthresh", None)
         ])
-    if params.get("norm_varthresh") is not None:
+    if params.get("norm_varthresh", None) is not None:
         cargs.extend([
             "-VarThreshN",
-            params.get("norm_varthresh")
+            params.get("norm_varthresh", None)
         ])
-    if params.get("corrmap") is not None:
+    if params.get("corrmap", None) is not None:
         cargs.extend([
             "-CorrMap",
-            params.get("corrmap")
+            params.get("corrmap", None)
         ])
-    if params.get("corrmask"):
+    if params.get("corrmask", False):
         cargs.append("-CorrMask")
-    if params.get("aexpr") is not None:
+    if params.get("aexpr", None) is not None:
         cargs.extend([
             "-Aexpr",
-            params.get("aexpr")
+            params.get("aexpr", None)
         ])
-    if params.get("cexpr") is not None:
+    if params.get("cexpr", None) is not None:
         cargs.extend([
             "-Cexpr",
-            params.get("cexpr")
+            params.get("cexpr", None)
         ])
-    if params.get("sexpr") is not None:
+    if params.get("sexpr", None) is not None:
         cargs.extend([
             "-Sexpr",
-            params.get("sexpr")
+            params.get("sexpr", None)
         ])
-    if params.get("hist") is not None:
+    if params.get("hist", None) is not None:
         cargs.extend([
             "-Hist",
-            params.get("hist")
+            params.get("hist", None)
         ])
     return cargs
 
@@ -280,9 +269,11 @@ def v_3d_tcorr_map_outputs(
 
 def v_3d_tcorr_map_execute(
     params: V3dTcorrMapParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dTcorrMapOutputs:
     """
+    3dTcorrMap
+    
     AFNI program to compute correlation maps of input time series data.
     
     Author: AFNI Developers
@@ -291,10 +282,12 @@ def v_3d_tcorr_map_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dTcorrMapOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TCORR_MAP_METADATA)
     params = execution.params(params)
     cargs = v_3d_tcorr_map_cargs(params, execution)
     ret = v_3d_tcorr_map_outputs(params, execution)
@@ -323,6 +316,8 @@ def v_3d_tcorr_map(
     runner: Runner | None = None,
 ) -> V3dTcorrMapOutputs:
     """
+    3dTcorrMap
+    
     AFNI program to compute correlation maps of input time series data.
     
     Author: AFNI Developers
@@ -363,8 +358,6 @@ def v_3d_tcorr_map(
     Returns:
         NamedTuple of outputs (described in `V3dTcorrMapOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_TCORR_MAP_METADATA)
     params = v_3d_tcorr_map_params(
         input_=input_,
         seed=seed,
@@ -384,13 +377,13 @@ def v_3d_tcorr_map(
         sexpr=sexpr,
         hist=hist,
     )
-    return v_3d_tcorr_map_execute(params, execution)
+    return v_3d_tcorr_map_execute(params, runner)
 
 
 __all__ = [
     "V3dTcorrMapOutputs",
-    "V3dTcorrMapParameters",
     "V_3D_TCORR_MAP_METADATA",
     "v_3d_tcorr_map",
+    "v_3d_tcorr_map_execute",
     "v_3d_tcorr_map_params",
 ]